Nickel in PDB 5dqw: The Crystal Structure of Bacillus Subtilis Ypgq in Complex with Adp

The structure of The Crystal Structure of Bacillus Subtilis Ypgq in Complex with Adp, PDB code: 5dqw was solved by Y.J.Jeon, W.S.Song, S.I.Yoon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.865, 52.499, 82.322, 90.00, 93.33, 90.00
R / Rfree (%)	20.9 / 26.1

The binding sites of Nickel atom in the The Crystal Structure of Bacillus Subtilis Ypgq in Complex with Adp (pdb code 5dqw). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the The Crystal Structure of Bacillus Subtilis Ypgq in Complex with Adp, PDB code: 5dqw:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the The Crystal Structure of Bacillus Subtilis Ypgq in Complex with Adp


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of The Crystal Structure of Bacillus Subtilis Ypgq in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni302 b:55.2 occ:1.00 NE2 A:HIS29 2.4 32.2 1.0 OD1 A:ASP124 2.4 37.6 1.0 O A:HOH401 2.6 38.3 1.0 NE2 A:HIS58 2.7 44.7 1.0 OD1 A:ASP59 2.9 50.9 1.0 OD2 A:ASP59 3.0 53.7 1.0 CG A:ASP124 3.2 35.9 1.0 OD2 A:ASP124 3.2 44.2 1.0 CE1 A:HIS29 3.3 37.3 1.0 CG A:ASP59 3.4 46.2 1.0 CD2 A:HIS29 3.4 32.2 1.0 CD2 A:HIS58 3.6 43.4 1.0 CE1 A:HIS58 3.7 45.0 1.0 ND1 A:HIS29 4.4 36.9 1.0 O A:HOH415 4.4 34.4 1.0 O3B A:ADP301 4.4 83.3 1.0 CG A:HIS29 4.5 35.2 1.0 CB A:ASP124 4.6 33.4 1.0 CD2 A:HIS25 4.7 55.8 1.0 O2B A:ADP301 4.8 84.6 1.0 CG A:HIS58 4.8 40.4 1.0 ND1 A:HIS58 4.8 44.1 1.0 O1B A:ADP301 4.8 83.9 1.0 PB A:ADP301 4.8 84.4 1.0 CB A:ASP59 4.9 42.8 1.0 CD1 A:ILE30 4.9 37.8 1.0

Nickel binding site 2 out of 2 in the The Crystal Structure of Bacillus Subtilis Ypgq in Complex with Adp


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of The Crystal Structure of Bacillus Subtilis Ypgq in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni302 b:74.4 occ:1.00 OD1 B:ASP124 2.5 59.2 1.0 NE2 B:HIS29 2.5 52.1 1.0 O B:HOH402 2.8 59.1 1.0 NE2 B:HIS58 2.9 64.5 1.0 OD1 B:ASP59 3.0 71.6 1.0 OD2 B:ASP59 3.1 70.4 1.0 CG B:ASP124 3.2 57.0 1.0 OD2 B:ASP124 3.2 65.0 1.0 CE1 B:HIS29 3.4 51.2 1.0 CG B:ASP59 3.4 66.7 1.0 CD2 B:HIS29 3.5 51.1 1.0 CE1 B:HIS58 3.7 63.8 1.0 CD2 B:HIS58 4.0 66.2 1.0 O1B B:ADP301 4.3 84.1 1.0 CD2 B:HIS25 4.3 79.4 1.0 ND1 B:HIS29 4.5 49.9 1.0 O2B B:ADP301 4.6 83.0 1.0 CG B:HIS29 4.6 51.6 1.0 CB B:ASP124 4.7 53.8 1.0 O B:HOH403 4.7 48.0 1.0 CD1 B:ILE30 4.8 57.0 1.0 ND1 B:HIS58 4.9 62.3 1.0 CB B:ASP59 4.9 65.5 1.0 PB B:ADP301 5.0 83.6 1.0

Y.J.Jeon, S.C.Park, W.S.Song, O.H.Kim, B.C.Oh, S.I.Yoon. Structural and Biochemical Characterization of Bacterial Ypgq Protein Reveals A Metal-Dependent Nucleotide Pyrophosphohydrolase J.Struct.Biol. V. 195 113 2016.
ISSN: ESSN 1095-8657
PubMed: 27062940
DOI: 10.1016/J.JSB.2016.04.002